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 U1A Protein Structure for Molecular Biology The U1A-RNA Complex. 
The U1A-RNA Complex is involved in the splicing of mRNA. The RNA-binding domain (RBD1) is shown using the Cartoon display. The protein is colored by Structure and the RNA is colored Shapely, with white backbone. The N- and C-termini are labeled. (cf. Fig. 4 of Oubridge et al.).
The domain has the RNP consensus sequence that is also found in more than 250 other protein sequences. This homologous sequence is proposed to fold into the conserved babbab fold seen here. (Color the structure by Group; click on the "Protein, only" button; and trace the chain from the blue N-terminus to the red C-terminus of the protein.)
Highlight the sidechains that interact with RNA.
Those residues that interact nonspecifically (bases or backbone phosphates) are colored white. The residues that interact specifically (H-bonds to bases) are colored red. The latter group is labelled at their a-carbons. Nucleotides at the top of the hairpin stem (Cyt 5-Gua 16) and the first loop nucleotide (Ade 6) are labelled. Zoom for a closer view of these contacts. (cf. Figs. 5 of Oubridge et al.)
Close-up view of the Arg52 H-bonding to Ade 6 and Gua 16.
The arginine and nucleotides are shown as Ball & Stick with CPK coloring. Some H-bond distances are indicated. (cf. Fig. 5a of Oubridge et al.)
Close-up view of the stacking interactions.
The sidechains of Tyr13, Phe56, and Asp102 are shown as Spacefill with CPK coloring. The bases of Cyt 10, Ade 11, and Cyt 12 are shown as Spacefill with Shapely coloring. Tyr13 stacks atop Cyt 10 and forms a perpendicular "aromatic-aromatic" interaction with Phe56. Phe56 and Asp102 sandwich the bases of Ade 11 and Cyt 12 in a four-member stack. (cf. Fig. 5e of Oubridge et al.)
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Coordinates from 1URN.pdb (Chains A & P, only of the trimeric crystal structure).
U1A-3'UTR Complex Structure is a one-page overview of the regulatory complex formed between two U1A molecules and its pre-mRNA.
Coordinates for the crystal structure of U1A without bound RNA are 1NRC.pdb; the reference is Nagai et al. (1990) Nature348 515.
Coordinates for the NMR solution structure of U1A without bound RNA are 1FHT.pdb; the reference is Avis et al. (1996) J. Mol. Biol.257 398.